I suspect this is not a theme issue, but a content type issue. Certain types of content have very different user metrics.
If you have lower quality articles with high bounce rate, high exit rate, low time on site, etc., moving them out to a subdomain might be a good idea. It'll take the toxicity out of the main domain, and averages will improve there.
This is like Adwords. Keywords with a low CTR and/or quality score should be separated out, because their poor metrics poison the whole campaign. Could be a case of Google taking practice from one area of its business and applying to another.